About a dozen refugees were asked to leave the Bellville Presbyterian church after being accused of stealing stored food and crockery.
But a Methodist minister in the area said there had also been problems with "local thugs" stealing from churches housing refugees.
The Bellville Presbyterian Church opened its doors and hearts to about 300 refugees after violent mobs chased them out of townships during last month's xenophobic attacks in townships around Cape Town.
The refugees, from Kalkfontein, Bloekombos and Wallacedene, had been housed in the church's hall from May 23, and, according to church elders, had started stealing church property and from each other a few days after moving in.
Presbyterian church elder John Kleynhans told Weekend Argus they had accepted the nearly 300 refugees in their church hall "out of the goodness of our hearts", but were appalled when they discovered a few had started stealing items from the church kitchen.
"Mainly the Somalis made a lot of trouble. They stole food and crockery out of the church cupboards and even stole from each other."
Kleynhans said the group stole the items at night, despite being given meals and warm drinks every day.
"We are very upset and disturbed by what had happened."
Kleyhans said the "group of thieves" was removed from the other refugees about two weeks ago.
He said they had either returned to the townships or had gone to one of the other safety camps.
Last Friday about 50 immigrants of the initial group of about 300 were moved from the church hall to the Methodist church in Bellville.
Kleynhans said the church could no longer accommodate them because the hall was booked for pension payouts and other activities this week.
Pastor Dave Stemmet, overseeing the group at the Methodist church hall, said it had become "very difficult" to accommodate the refugees.
The church was feeding and housing them without assistance from the City of Cape Town or the province.
"We will have to look at options to relocate these immigrants as soon as possible."
Stemmet said when the refugees were being housed at the Presbyterian church hall, local thugs had entered the hall and had robbed and harassed immigrants.
"Some of the refugees stole food and other items, but there was also an outside element of locals who came to steal, especially at night. The incidents were reported to police and it eventually stopped."
This article was originally published on page 6 of The Cape Arg
